{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/checksum.txt"],"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062611-1A.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062614-1A.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062612-1A.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062613-1A.msf"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062614-1A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062612-1A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062611-1A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062613-1A.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062614-1A.pdResult","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062613-1A.pdResult","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062612-1A.pdResult","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073111/480_FPEP240062611-1A.pdResult"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["shuguozh@tmmu.edu.cn"],"submitter":["Huizhen Zou"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073111"],"tissue":["Cell Culture"],"sample_protocol":["\"1.Cell Culture and Lysis: HCCLM3 cells were cultured to the logarithmic growth phase. Cells were harvested and lysed to extract total proteins, which were then equally divided into two aliquots. 2.Compound Treatment: Ginkgolic Acid was added to the treatment group and an equivalent volume of DMSO to the control group to a final concentration of 30 μM. The mixtures were incubated on a shaker at room temperature for 30 minutes. 3.Limited Proteolysis: Proteinase K was added to both groups, and the reaction was carried out on ice for 10 minutes to achieve limited digestion. 4.Reaction Termination: The digestion was immediately terminated by adding a protease inhibitor cocktail. 5.Denaturation:：6x loading buffer was added to the samples, followed by denaturation at 70°C in a metal bath for 5 minutes. 6.Electrophoresis and Staining: The samples were separated by SDS-PAGE and visualized using Coomassie Brilliant Blue staining. 7.In-Gel Digestion: Differential protein bands were excised from the gel and subjected to in-gel digestion for subsequent LC-MS/MS analysis. 8.Enzymatic hydrolysis process within the gel: Add 100 mM of TEAB buffer and 1 μg of trypsin to the gel particles, then add 1/300 cacl2 and enzymatize at 37°C overnight. Centrifuge at low speed to collect the supernatant. Add acetonitrile to the gel particles, vortex and shake to centrifuge. Take the supernatant, add 0.1% formic acid to the gel, shake at room temperature for 5 minutes, then centrifuge at low speed to collect the supernatant. Combine the supernatant and freeze-dry it. Redissolve in 0.1% formic acid aqueous solution, mix well, and centrifuge at 12000 g at room temperature for 5 minutes. Take the supernatant and slowly pass it through a C18 deionization column. Then, continuously wash three times with cleaning solution (0.1% formic acid, 3% acetonitrile), add an appropriate amount of eluent (0.1% formic acid, 70% acetonitrile), collect the filtrate, and freeze-dry it. 9.LC Analysis:Mobile phase A (100% water, 0.1% formic acid) and B solution (80% acetonitrile, 0.1% formic acid) were prepared. The lyophilized powder was dissolved in 10 μL of solution A,centrifuged at 14000 g for 20 min at 4℃, and 1 μg of sample was injected into EASY-nLCTM 1200 nano-upgraded UHPLE system with a home-made C18 Nano-Trap column (4.5 cm×75 μm,3 μm). Peptides were separated in a home-made analytical column (15 cm×150 μm, 1.9 μm),using a linear gradient elution 10.MS Analysis:The separated peptides were analyzed by Q ExactiveTM HF-X mass spectrometer, with ion source of Nanospray Flex™（ESI）, spray voltage of 2.1 kV and ion transport capillary temperature of 320°C. Full scan ranges from m/z 350 to 1500 with resolution of 60000 (at m/z 200), an automatic gain control (AGC) target value was 3×10^6 and a maximum ion injection time was 20 ms. The top 40 precursors of the highest abundant in the full scan were selected and fragmented by higher energy collisional dissociation (HCD) and analyzed in MS/MS, where resolution was 15000 (at m/z 200), the AGC target value was 1×10^5, the maximum ion injection time was 45 ms,a normalized collision energy of 27%, an intensity threshold of 2.2×10^4, and the dynamic exclusion parameter of 20 s. The raw data of MS detection was named “.raw”.\""],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["\"The resulting spectra from each fraction were searched separately against homo_sapiens_uniprot_2023_10_18_Swissprot.fasta(20427 sequences)database by the search engines: Proteome Discoverer. The search parameters are set as follows: mass tolerance for precursor ion was 10 ppm and mass tolerance for product ion was 0.02 Da. Carbamidomethyl was specified as fixed modifications, Oxidation of methionine (M) was specified as dynamic modification, and loss of methionine at the N-Terminal. A maximum of 2 missed cleavage sites were allowed. In order to improve the quality of analysis results, the software PD further filtered the retrieval results: Peptide Spectrum Matches (PSMs) with a credibility of more than 99% was identified PSMs. The identified protein contains at least 1 unique peptide. The identified PSMs and protein were retained and performed with FDR no more than 1.0%. \""],"omics_type":["Proteomics"],"labhead":["shuguo zheng"],"instrument_platform":[""],"labhead_affiliation":["Department of Hepatobiliary Surgery, the First Affiliated Hospital(Southwest Hospital) of Army Military Medical University, Chongqing 400038, China."],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["41877645 Liu R, Zhang Y, Zou H, Zhang M, Yang Z, Liao K, Wang G, Liu B, Tang L, Kang X, Zheng S. Ginkgolic acid targets HSPA8 to trigger ferroptosis in hepatocellular carcinoma <i>via</i> chaperone-mediated autophagy-dependent GPX4 degradation. Pharm Biol. 2026 64(1):514-535 10.1080/13880209.2026.2646350"],"submitter_mail":["zouhuizhen1998@gmail.com"],"submitter_affiliation":["THE GENERAL HOSPITAL OF WESTERN THEATER COMMAND PLA"],"submitter_country":["China"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic Analysis of Ginkgolic Acid Targets in HCCLM3 Cells via DARTS-LC-MS/MS","description":"This study aims to identify the potential protein targets of Ginkgolic Acid in human hepatocellular carcinoma HCCLM3 cells using the Drug Affinity Responsive Target Stability (DARTS) assay combined with LC-MS/MS proteomics. Whole cell lysates from Ginkgolic Acid-treated and vehicle control (DMSO) HCCLM3 cells were subjected to limited proteolysis with proteinase K. The digested protein samples were separated by SDS-PAGE, and differential protein bands were excised, digested in-gel, and analyzed by mass spectrometry. The raw data will be used to identify proteins whose stability is altered upon Ginkgolic Acid binding, providing insights into its anti-tumor mechanisms.","dates":{"publication":"2026-03-30","submission":"2026-01-15"},"accession":"PXD073111","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:192875","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:658457","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:5759","NEWT:1736231","NEWT:1392","NEWT:498217","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:935293","NEWT:375146","NEWT:118698","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1513458","NCBITaxon:40559","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:4093","NEWT:4096","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:40479","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:1268063","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:1194669","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","NEWT:89453","NEWT:287889","NEWT:51515","NEWT:588596","NEWT:51511","NEWT:8845","NEWT:92867","NEWT:92866","NEWT:5334","NEWT:51750","NEWT:202950","NEWT:382352","NEWT:413071","NEWT:632957","NEWT:9925","NEWT:89462","NEWT:8839","NEWT:90690","NEWT:4232","NEWT:2758385","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:312017","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:284593","NEWT:100392","NEWT:5315","NEWT:9913","NEWT:265872","NEWT:105841","NEWT:337330","NEWT:2666255","NEWT:2285","NEWT:999810","NCBITaxon:5693","NEWT:1392998","NEWT:380394","NEW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